Williams, who won her 23rd Grand Slam title at the Australian Open this year, confirmed her pregnancy in April and said she would miss the remainder of the 2017 season to give birth.
The former world number one is intending to return to the sport next year but Clijsters has her doubts on whether the American will be able to dominate like she has for many, many years.
Belgium's ex-number one made the 'Mother of all Comebacks' when making a sensational return in 2009 to clinch the US Open title, just 18 months after giving birth to her first baby.
The 34-year-old, who retired at the age of 29 with four Slam titles to her name, has warned Williams there will be several challenges along the way if she decides to make a comeback.
"Every player is different, every pregnancy is different, every delivery is different so it's really hard to comment on how quickly she'll be able to bounce back," Clijsters was quoted as saying by Sport24. "Tennis-wise, she won 23 Grand Slams before she went to have her baby. I (had) won one, so I think she has that part completely covered, no problem with the Grand Slams.
"But you have to find your way, especially as a first-time mother. I had a little bit of help too. My husband was able to travel with me. I wouldn't be able to do it if my family wasn't there.
"So, it also depends on the situation and on how they see themselves as a mother and athlete. And I'm sure there'll be challenges ahead."